Soybean cyst nematode (SCN) is currently the most devastating pathogen of soybean. SCN penetrates the root and migrates toward the central vascular bundle where it establishes a complex multinucleated feeding structure that withdraws nutrients from the plant to support development and growth of the nematode. To identify genes that may play significant roles in formation and maintenance of the feeding structure, RNA from SCN inoculated and non-inoculated root pieces were hybridized to the Affymetrix soybean genome GeneChips. RNA was collected at 8, 12 and 16 dpi from root pieces (1 to 3 mm) that displayed multiple swollen female SCN and similar root pieces from non-inoculated roots. Branch roots and root tips were trimmed from the root pieces to minimize the amount of RNA contributed by these organs. Of the 35,593 transcripts represented on the chip, approximately 26,500 were expressed in the SCN colonized root pieces. ANOVA followed by False Discovery Rate (FDR) analysis indicated that 4,616 transcripts changed significantly (Q-value < 0.05) in response to inoculation with SCN. 515 transcripts increased more than 2-fold and 98 decreased more than 2-fold in SCN colonized root pieces compared to non-inoculated root pieces. Of the transcripts to which a function can be assigned, a large proportion of these were associated with cell wall structure. Other functional categories that included a large number of up-regulated transcripts were defense and metabolism, and a smaller group of transcripts were associated with signal transduction and transcription.